Mercurial > repos > tomnl > create_sqlite_db
comparison track_rt_raw.R @ 0:fe7d7cc95ca5 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
| author | tomnl |
|---|---|
| date | Tue, 27 Mar 2018 06:03:50 -0400 |
| parents | |
| children | 1a88758357ed |
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| -1:000000000000 | 0:fe7d7cc95ca5 |
|---|---|
| 1 library(optparse) | |
| 2 library(xcms) | |
| 3 option_list <- list( | |
| 4 make_option(c("--xset_path"), type="character"), | |
| 5 make_option(c("-o", "--out_dir"), type="character") | |
| 6 ) | |
| 7 | |
| 8 # store options | |
| 9 opt<- parse_args(OptionParser(option_list=option_list)) | |
| 10 | |
| 11 load(opt$xset_path) | |
| 12 | |
| 13 print(xset) | |
| 14 | |
| 15 rtraw <- xset@peaks[,c('rt', 'rtmin', 'rtmax')] | |
| 16 colnames(rtraw) <- c('rt_raw','rtmin_raw','rtmax_raw') | |
| 17 xset@peaks <- cbind(xset@peaks, rtraw) | |
| 18 | |
| 19 | |
| 20 print('saving RData') | |
| 21 save.image(file.path(opt$out_dir, 'xset_rt_raw_tracked.RData')) |